When a research peptide is described as “99% pure,” that number almost always comes from high-performance liquid chromatography, or HPLC. It is a useful figure, but only if you know what it measures and what it leaves out.
How HPLC works, briefly
A small sample of dissolved peptide is pushed through a column under pressure. Different molecules travel through at different speeds, so they separate and reach a detector at different times. The detector draws a chromatogram: a line with peaks, where each peak represents a component of the sample.
What the purity percentage means
Purity is usually calculated as the area of the main peak divided by the total area of all peaks, expressed as a percentage. A result of 99% means that 99% of the detected signal belongs to the target peptide and 1% belongs to other detected components, such as truncated or deletion sequences from synthesis.
What it does not tell you
- Total peptide content. Water and counter-ions, such as acetate or trifluoroacetate, are not always visible in the chromatogram, so a vial can be highly pure yet contain less peptide by weight than the label amount implies.
- Identity. HPLC shows how many components are present, not what they are. Identity is confirmed separately, typically by mass spectrometry.
- Anything the detector cannot see. Components that do not absorb at the chosen wavelength will not show up.
Details worth checking
- The detection wavelength, commonly around 214 to 220 nm for peptides.
- The column and gradient used, since different methods can resolve different impurities.
- A full chromatogram, not just a single number. A clean, sharp main peak with a flat baseline is a good sign.
- The lot number on the report matching the vial in your hands.
Pair it with mass spectrometry
Purity and identity answer different questions, and a good analysis report includes both. Our guide to reading a certificate of analysis shows how the pieces fit together.
Browse our catalog of lyophilized research compounds.
For laboratory research use only. Not for human or veterinary use. This article is general educational information for researchers and is not medical advice.